Bacterial blight (Xanthomonas arboricola pv.juglandis) is one of the main diseases of walnut that reduce the yield in the central, western and northern regions of Iran. This disease was first reported form, Qazvin and Mazandaran, then widely reported from northern, central and western provinces. To identify the cause of the disease in different provinces, infected leaves collected from Alborze, Lorestan and Kurdestan provinces during spring-summer . Based on the conventional methods of bacteriology, some strains purified and Pathogenicity was proved on three-year plant leaves and on detached fruits of walnut. Based on the biochemical and pathogenesity tests, the yellow colored colonies identified as Xanthomonas arboricola pv. juglandis. According to the results of cluster analysis model of the rep-PCR method, the strains were categorized in three groups with similarity. On the basis of the sequence of RNA polymerase, beta subunit and dendrogram of NJ method, the strains were differentiated in a separate category. Three strains ( , and ) were collected from Lorestan and Kordestan and completely separated from other Xanthomonas in independent group